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Description
Only very few reads filtered out by low complexity end in failed_out, at least with the correct reason ("failed_low_complexity"). Likely, they failed by another reason but online one reason is written. It would be good to have the same number of reads annotated with "failed_low_complexity" as the statistics reports.
Example:
Filtering result:
reads passed filter: 152964
reads failed due to low quality: 6976
reads failed due to too many N: 0
reads failed due to too short: 26046
reads failed due to low complexity: 3728
seqkit grep -n -r -p 'failed_low_complexity' ${PREFIX}_trimmed_failed.fastq.gz
@M04903:348:000000000-GMNJP:1:1101:3861:18025 2:N:0:12 failed_low_complexity
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+
ABA?ADABDDDBEEEEGGGG?@E>@EEEG?CGGCCGGGC-@::@BG@GB@B?BB?BB??BB9B;
@M04903:348:000000000-GMNJP:1:1103:15515:16026 2:N:0:12 failed_low_complexity
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+
ABBAABBDDBBBGGGGGGCGGGGF@EEEGCCGGGGGGCGGGGCCBGGGGGFB?FFFFAF@
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